Among the genes identified by microarray analysis, some genes demonstrated dramatic expression level changes in response to the combination of more than one factor.
The patterns of expression for these genes demonstrated by microarray analysis were confirmed by qRT-PCR (Table 3).
Using the 'Significance Analysis of Microarrays' strategy [ 30], 3109 genes demonstrated consistent expression changes and acceptable spot confidence of which 2957 had appropriate q-values (<0.1%).
Previous work using microarrays to identify H. pylori-regulated genes demonstrated increased uPA in gastric cancer cell lines (32), and there has been work using gastric cancer cell lines that indicates H. pylori stimulation of uPA, uPAR, and PAI-1 expression (24, 30, 31).
Genes demonstrated regulation consistently across quadruplicate microarray experiments.
Genes demonstrated to be differentially expressed following microarray analysis of TCC senescence are coloured in grey.
The 10 genes demonstrated similar expression patterns in the microarray and the RT-qPCR analysis (Additional file 17).
In total, 1,036 genes demonstrated a significant upregulation or downregulation based on the microarray results.
All four candidate genes demonstrated the same expression trends to those identified by microarray assay.
Within the ovary-upregulated category, we randomly chose two of the top 200 most upregulated genes, in order to assess the accuracy of microarray results for genes demonstrating less striking differences in expression.
